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<i>Epimedium wushanense</i> (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of <i>E. wushanense</i> and its closely related species, namely, <i>E</i>. <i>pseudowushanense</i>, <i>E. chlorandrum</i>, <i>E. mikinorii</i>, <i>E. ilicifolium</i>, and <i>E. borealiguizhouense</i>. These species are often confused with one another because of their highly similar morphological characteristics. This confusion leads to misuse in the medicinal market threatening efficiency and safety. Here, we studied the plastid genomes of these <i>Epimedium</i> species. Results show that the plastid genomes of <i>E. wushanense</i> and its relative species are typical circular tetramerous structure, with lengths of 156,855&#8722;158,251 bp. A total of 112 genes were identified from the <i>Epimedium</i> plastid genomes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A loss of <i>rpl32</i> gene in <i>E. chlorandrum</i> was found for the first time in this study. The phylogenetic trees constructed indicated that <i>E. wushanense</i> can be distinguished from its closely related species. <i>E. wushanense</i> shows a closer relationship to species in ser. <i>Dolichocerae</i>. In conclusion, the use of plastid genomes contributes useful genetic information for identifying medicinally important species <i>E. wushanense</i> and provides new evidence for understanding phylogenetic relationships within the <i>Epimedium</i> genus.